This chest is locked away behind a wolf door in the area, and can only be opened once you have the Wolf Form ability.

Kitchen

Work your way around towards the left of the area and you'll soon come to an upward climb with steam pipes lining the walls. Climb this one and pull the lever above. This raises the water level in that big and seemingly empty room next to shaft you just climbed up from. Jump back down, dive and swim left.

Toy Maker's Workshop

Demon Wings ability required. In the central area where you can climb down a green scaffold into a massive electric pit with some moving platforms. There is a ledge across from the scaffold. Double jump and glide to it then phase through the door with Mist Form.

Vampire's Tower

Coming from the Resurrection Room, follow the path about halfway until reach the two sets of steps. Stand on the left one and double jump to to reach the ledge above. Keep heading right all the way to a wolf door at the end.

Throne Entrance

This one is found off to the right surrounded by Shadow Claw walls, if you drop down from the broken stairs.

Locked behind a sacred stone door. You must first receive the upgrade for the Combat Cross that allows Trevor to yank these doors apart to get this chest.

Cells

Just past the second lift to the left is a door that requires Shadow Magic to open. This chest is behind it.

Vertical Prison

Locked behind a sacred stone door. You must first receive the upgrade for the Combat Cross that allows Trevor to yank these doors apart to get this chest.

Abandoned Mine

Locked behind a sacred stone door near the beginning of the area. You must first receive the upgrade for the Combat Cross that allows Trevor to yank these doors apart to get this chest.

Abandoned Mine

On the way to the red teleporter, drop off from the magnetic rail just before you reach the last fire-breathing dragon skull, you will land on a mine cart which you can then ride over to this subweapon upgrade chest.